Natural Product: NPC189782

Natural Product IDNPC189782
Common Name
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The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 DCYAJVOKJAFSES-HNNXBMFYSA-N
IUPAC Name n.a.
Synonyms (-)-Cornigerine
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL282984
PubChem CID 10000015
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000296] Benzodioxoles

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey DCYAJVOKJAFSES-HNNXBMFYSA-N
Standard InCHI InChI=1S/C21H21NO6/c1-11(23)22-15-6-4-12-8-18-20(28-10-27-18)21(26-3)19(12)13-5-7-17(25-2)16(24)9-14(13)15/h5,7-9,15H,4,6,10H2,1-3H3,(H,22,23)/t15-/m0/s1
SMILES CC(=N[C@H]1CCc2cc3c(c(c2-c2ccc(c(=O)cc12)OC)OC)OCO3)O

  Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO4250 Gloriosa superba Species Colchicaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s10529-006-0004-9]
NPO24146 Colchicum brachyphyllum Species Colchicaceae Eukaryota n.a. Jordanian n.a. PMID[15730238]
NPO22241 Alangium villosum Species Cornaceae Eukaryota stem bark Ceram, Indonesia 1998 PMID[18327911]
NPO22241 Alangium villosum Species Cornaceae Eukaryota n.a. n.a. n.a. PMID[32372642]
NPO4250 Gloriosa superba Species Colchicaceae Eukaryota n.a. n.a. n.a. PMID[32372642]
NPO4250 Gloriosa superba Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24146 Colchicum brachyphyllum Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22241 Alangium villosum Species Cornaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4250 Gloriosa superba Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4250 Gloriosa superba Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4250 Gloriosa superba Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24146 Colchicum brachyphyllum Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22241 Alangium villosum Species Cornaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



  NP Quantity Composition/Concentration

Organism ID Organism Name Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



 Biological Activity

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT3597 Individual protein Tubulin beta chain Bos taurus Tubulin binding = 59.0 % PMID[3560165]
NPT3597 Individual protein Tubulin beta chain Bos taurus IC50 = 2100.0 nM PMID[17650015]
NPT518 Protein complex Tubulin Homo sapiens Binding = 59.0 % PMID[6620299]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT168 Cell line P388 Mus musculus Potency < 10.0 uM kg-1 PMID[19604701]
NPT83 Cell line MCF7 Homo sapiens EC50 = 61.0 nM PMID[17253840]
NPT397 Cell line NCI-H460 Homo sapiens EC50 = 59.0 nM PMID[24900865]
NPT395 Cell line SF-268 Homo sapiens EC50 = 97.0 nM PMID[23062825]
NPT137 Cell line L1210 Mus musculus IC50 = 20.0 nM PMID[32432867]
NPT729 Organism Micrococcus luteus Micrococcus luteus MIC > 500.0 ug.mL-1 PMID[12699389]
NPT21 Organism Aspergillus niger Aspergillus niger MIC > 500.0 ug.mL-1 DrugMatrix in vitro pharmacology data
NPT602 Organism Mycobacterium smegmatis Mycobacterium smegmatis MIC > 500.0 ug.mL-1 PMID[27492195]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae MIC > 500.0 ug.mL-1 PMID[22148427]
NPT2 Others Unspecified n.a. Activity = 50.0 % DrugMatrix in vitro pharmacology data

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT32 Organism Mus musculus Mus musculus T/C = 166.0 n.a. PMID[3560165]
NPT32 Organism Mus musculus Mus musculus MED > 0.4 mg kg-1 PMID[3560165]





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference
- Artemia LC50 = 7.7 ug.mL-1 PMID[15787448]

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC189782 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
0.8387 Intermediate Similarity NPC108957
0.8387 Intermediate Similarity NPC14005
0.8387 Intermediate Similarity NPC226941
0.6866 Remote Similarity NPC44642
0.6667 Remote Similarity NPC66678
0.6571 Remote Similarity NPC202839
0.507 Remote Similarity NPC600354
0.5067 Remote Similarity NPC609718

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC189782 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.8387 Intermediate Similarity NPD5089 Approved
0.8387 Intermediate Similarity NPD5090 Phase 4
0.6463 Remote Similarity NPD6841 Approved
0.6463 Remote Similarity NPD6842 Approved
0.6463 Remote Similarity NPD6843 Phase 3
0.5915 Remote Similarity NPD4055 Phase 2

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data